Stothard Research Group - CGView Server

Examples

Example 1

Comparing the Reclinomonas americana mitochondrial genome to proteins encoded by the Arabidopsis thaliana mitochondrial genome, the E. coli genome, and the human mitochondrial genome. The outermost two rings show features extracted from the Reclinomonas americana mitochondrial genome GenBank file. The next three rings show the positions of BLAST hits detected by blastx searches against the three comparison protein sets. The height of each arc in the BLAST results rings is proportional to the percent identity of the hit. Overlapping hits appear as darker arcs.

Files

Genome sequence: Reclinomonas americana mitochondrial sequence (NC_001823.gbk)

BLAST 1: Arabidopsis thaliana mitochondrial proteins (A_thaliana.fasta)

BLAST 2: Escherichia coli K12 proteins (E_coli.fasta)

BLAST 3: Homo sapiens mitochondrial proteins (H_sapiens.fasta)

Settings 1

Sequence file: NC_001823.gbk (format: genbank, length: 69034)

Global Blast Settings: query_split_size=50000, overlap_split_size=0

Blast 1: A_thaliana.fasta, blastx, expect=0.00001, Standard, filter=Yes

Blast 2: E_coli.fasta, blastx, expect=0.00001, Bacterial and Plant Plastid, filter=Yes

Blast 3: H_sapiens.fasta, blastx, expect=0.00001, Standard, filter=Yes

Map title: Untitled

Show GenBank/EMBL features: Yes

Show GC content: No

Show GC skew: No

Draw divider rings: Yes

Use opacity for BLAST hits: Yes

Show labels: Yes

Show ORFs: No

Show start and stop codons: No

Show blast hits by reading frame: No

Show legend: Yes

Font size: small

Tick density: 0.6

Draw features as: Arrows

View: Full size

Settings 2

Sequence file: NC_001823.gbk (format: genbank, length: 69034)

Global Blast Settings: query_split_size=50000, overlap_split_size=0

Blast 1: A_thaliana.fasta, blastx, expect=0.00001, Standard, filter=Yes

Blast 2: E_coli.fasta, blastx, expect=0.00001, Bacterial and Plant Plastid, filter=Yes

Blast 3: H_sapiens.fasta, blastx, expect=0.00001, Standard, filter=Yes

Map title: Untitled

Show GenBank/EMBL features: Yes

Show GC content: No

Show GC skew: No

Draw divider rings: Yes

Use opacity for BLAST hits: Yes

Show labels: Yes

Show ORFs: No

Show start and stop codons: No

Show blast hits by reading frame: No

Show legend: Yes

Font size: small

Tick density: 0.6

Draw features as: Arrows

View: Zoomed (8 times) on base 65000

Example 2

Comparing a known genome sequence to 454 Sequencing sequence reads. The outermost two rings show features extracted from the Francisella tularensis genome GenBank file. The next three rings show the positions of BLAST hits detected through blastn comparisons of the sequence against itself and two sets of 454 reads. The self comparison is used to highlight enriched sequences and to reveal sequences removed by the low-complexity sequence filter. The height of each arc in the BLAST results rings is proportional to the percent identity of the hit. Overlapping hits appear as darker arcs. The next two rings show GC content and GC skew. Each is plotted as the deviation from the average for the entire sequence.

Files

Genome sequence: Francisella tularensis subsp. tularensis (NC_006570.gbk)

BLAST 1: Francisella tularensis subsp. tularensis (NC_006570.fasta)

BLAST 2: 454 reads 1 (454_reads_1.fasta)

BLAST 3: 454 read 2 (454_reads_2.fasta)

Settings 1

Sequence file: NC_006570.gbk (format: genbank, length: 1892819)

Global Blast Settings: query_split_size=50000, overlap_split_size=0

Blast 1: NC_006570.fasta, blastn, expect=0.00001, Bacterial and Plant Plastid, filter=Yes

Blast 2: 454_reads_1.fasta, blastn, expect=0.00001, Bacterial and Plant Plastid, filter=Yes

Blast 3: 454_reads_2.fasta, blastn, expect=0.00001, Bacterial and Plant Plastid, filter=Yes

Map title: Untitled

Show GenBank/EMBL features: Yes

Show GC content: Yes

Show GC skew: Yes

Draw divider rings: Yes

Use opacity for BLAST hits: Yes

Show labels: No

Show ORFs: No

Show start and stop codons: No

Show blast hits by reading frame: No

Show legend: Yes

Font size: medium

Tick density: 0.6

Draw features as: Arrows

View: Full size

Settings 2

Sequence file: NC_006570.gbk (format: genbank, length: 1892819)

Global Blast Settings: query_split_size=50000, overlap_split_size=0

Blast 1: NC_006570.fasta, blastn, expect=0.00001, Bacterial and Plant Plastid, filter=Yes

Blast 2: 454_reads_1.fasta, blastn, expect=0.00001, Bacterial and Plant Plastid, filter=Yes

Blast 3: 454_reads_2.fasta, blastn, expect=0.00001, Bacterial and Plant Plastid, filter=Yes

Map title: Untitled

Show GenBank/EMBL features: Yes

Show GC content: Yes

Show GC skew: Yes

Draw divider rings: Yes

Use opacity for BLAST hits: Yes

Show labels: Yes

Show ORFs: No

Show start and stop codons: No

Show blast hits by reading frame: No

Show legend: Yes

Font size: medium

Tick density: 0.6

Draw features as: Arrows

View: Zoomed (8 times) on base 1040000

Example 3

Visualizing features of the Methanobacterium thermoautotrophicum genome, and comparing the DNA sequence to proteins encoded by three other methanogens. The contents of the feature rings (starting with the outermost ring) are as follows:

Ring 1: Forward strand features from Methanobacterium thermoautotrophicum GenBank file.
Rings 2,3,4: Forward strand ORFs in reading frames 3,2,1.
Rings 5,6,7: Forward strand start and stop codons in reading frames 3,2,1.
Rings 8,9,10: Reverse strand ORFs in reading frames 1,2,3.
Rings 11,12,13: Reverse strand start and stop codons in reading frames 1,2,3.
Ring 14: Reverse strand features from Methanobacterium thermoautotrophicum GenBank file.
Rings 15,16,17,18,19,20: BLAST hits obtained from blastx search of Methanobrevibacter smithii proteins, in which the query was translated in reading frames 3,2,1,-1,-2,-3.
Rings 21,22,23,24,25,26: BLAST hits obtained from blastx search of Methanococcus jannaschii proteins, in which the query was translated in reading frames 3,2,1,-1,-2,-3.
Rings 27,28,29,30,31,32: BLAST hits obtained from blastx search of Methanococcus maripaludis proteins, in which the query was translated in reading frames 3,2,1,-1,-2,-3.

Files

Genome sequence: Methanobacterium thermoautotrophicum str. Delta H (NC_000916.gbk)

BLAST 1: Methanobrevibacter smithii proteins (Mb_smithii.fasta)

BLAST 2: Methanococcus jannaschii proteins (Mc_jannaschii.fasta)

BLAST 3: Methanococcus maripaludis proteins (Mc_maripaludis.fasta)

Settings 1

Sequence file: NC_000916.gbk (format: genbank, length: 1751377)

Global Blast Settings: query_split_size=50000, overlap_split_size=0

Blast 1: Mb_smithii.fasta, blastx, expect=0.00001, Bacterial and Plant Plastid, filter=Yes

Blast 2: Mc_jannaschii.fasta, blastx, expect=0.00001, Bacterial and Plant Plastid, filter=Yes

Blast 3: Mc_maripaludis.fasta, blastx, expect=0.00001, Bacterial and Plant Plastid, filter=Yes

Show GenBank/EMBL features: Yes

Draw divider rings: Yes

Use opacity for BLAST hits: No

Show labels: No

Show ORFs (over 100 codons) and display them separated.

Show start and stop codons: Yes

Start codons: atg|ttg|att|gtg|ctg

Stop codons: taa|tag|tga

Show blast hits by reading frame: Yes

Show legend: Yes

Font size: medium

Tick density: 0.6

Draw features as: Arrows

View: Full size

Settings 2

Sequence file: NC_000916.gbk (format: genbank, length: 1751377)

Global Blast Settings: query_split_size=50000, overlap_split_size=0

Blast 1: Mb_smithii.fasta, blastx, expect=0.00001, Bacterial and Plant Plastid, filter=Yes

Blast 2: Mc_jannaschii.fasta, blastx, expect=0.00001, Bacterial and Plant Plastid, filter=Yes

Blast 3: Mc_maripaludis.fasta, blastx, expect=0.00001, Bacterial and Plant Plastid, filter=Yes

Show GenBank/EMBL features: Yes

Draw divider rings: Yes

Use opacity for BLAST hits: No

Show labels: Yes

Show ORFs (over 100 codons) and display them separated.

Show start and stop codons: Yes

Start codons: atg|ttg|att|gtg|ctg

Stop codons: taa|tag|tga

Show blast hits by reading frame: Yes

Show legend: Yes

Font size: medium

Tick density: 0.6

Draw features as: Arrows

View: Full size

View: Zoomed (20 times) on base 1605000

Example 4

Visualizing features and analysis results supplied as GFF files. The outermost feature ring shows features described in the pBluescript_features.gff file. The next ring shows score values obtained from the pBluescript_scores.gff file. The dashed line represents a score of 0, and positive values are shown in green, and negative values in pink. The height of each arc in the score plot is proportional to the magnitude of the score value. The next two rings show GC content and GC skew. Each is plotted as the deviation from the average for the entire sequence.

Files

Genome sequence: pBluescript II KS(-) (pBluescript.fasta)

Gene information: features (pBluescript_features.gff)

Analysis information: scores (pBluescript_scores.gff)

Settings 1

Sequence file: pBluescript.fasta (format: fasta, length: 2961)

Gene file: pBluescript_features.gff

Analysis file: pBluescript_scores.gff

Map title: Untitled

Show GenBank/EMBL features: Yes

Show GC content: Yes

Show GC skew: Yes

Draw divider rings: Yes

Use opacity for BLAST hits: Yes

Show labels: Yes

Show ORFs: No

Show start and stop codons: No

Show blast hits by reading frame: No

Show legend: Yes

Font size: medium

Tick density: 0.6

Draw features as: Arrows

View: Full size

Complex Maps

For publication purposes we can provide much more complex and customizable maps than the CGView Server, using an in-house pipeline we have developed. These maps can include COG assignments, base composition plots, gene expression results, and BLAST comparisons with up to 100 genomes on a single map. The BLAST comparisons can be conducted using DNA or translated DNA, or by using the translations of CDS features or ORFs. An improved color scheme that is more easily viewed and interpreted in publications is used for the BLAST results. For examples of what our pipeline can generate, see the "Examples from our CGView Pipeline" section in the CGView Gallery. To request a map contact Paul Stothard with a brief description of the genome sequence you have and the information you would like the map to depict (BLAST comparisons of CDS translations with those from all other genomes in the genus for example).